[phenixbb] red blobs (Andrea Smith)

[Mitchell D. Miller]

Hi Andrea,

   You can also put a few zero occupancy atoms in the negative
density to force phenix.refine to exclude the region
from the bulk solvent mask.

(You may also need to set
refinement.mask.ignore_zero_occupancy_atoms = False
so that the zero occupancy atoms are included in the mask)

Regards,
Mitch



Quoting Kay Diederichs <kay.diederichs at uni-konstanz.de>:

> Hi Andrea,
>
> hmm, did phenix.refine actually use optimize_mask=true ?
>
> If you compare the logfiles of phenix.refine (for the default run  
> with opimize_mask=false, and the new run with optimize_mask=true)  
> side-by-side with xxdiff or vimdiff (yes this needs to be run from a  
> command-line) then there should be a difference.
>
> Making peace with the red blobs is somewhat unsatisfactory from a  
> technical viewpoint, but probably not relevant from a biological one.
>
> I'd guess that the authors of  
> https://journals.iucr.org/a/issues/2024/02/00/pl5035/index.html  
> would be interested to look at your case ...
>
> Best wishes,
> Kay
>
>
> Am 15.03.24 um 08:27 schrieb Andrea Smith:
>> Hi Kay,
>>
>> I tried the mask optimization and there is no change in how the  
>> final map looks like.
>>
>> Should I just make peace with it?
>>
>> Best,
>> Andrea
>>
>> On Thursday, March 14, 2024 23:11 CET, Kay Diederichs  
>> <kay.diederichs at uni-konstanz.de> wrote:
>>> Hi Andrea,
>>>
>>> in your case, phenix.refine seems to fill bulk solvent into volumes that
>>> are not actually filled by solvent.
>>> It might help to optimize the mask, see
>>> https://phenix-online.org/documentation/reference/refinement.html#bulk-solvent-correction-and-anisotropic-scaling
>>> "6. Mask parameters".
>>>
>>> Best,
>>> Kay
>>> --
>>> Kay Diederichs http://strucbio.biologie.uni-konstanz.de
>>> email: Kay.Diederichs at uni-konstanz.de Tel +49 7531 88 4049
>>> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
>>>
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>
> -- 
> Kay Diederichs                http://strucbio.biologie.uni-konstanz.de
> email: Kay.Diederichs at uni-konstanz.de             Tel +49 7531 88 4049
> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
>
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